The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species
Scientific Reports, 2022 Identification of genetic variations is a central part of population and quantitative genomics studies based on high-throughput sequencing data. Even though popular variant callers such as Bcftools mpileup and GATK HaplotypeCaller were developed nearly ...
Kiwoong Nam
exaly +2 more sources
Comparison of GATK and DeepVariant by trio sequencing
Scientific Reports, 2022 While next-generation sequencing (NGS) has transformed genetic testing, it generates large quantities of noisy data that require a significant amount of bioinformatics to generate useful interpretation.
Wuh-liang Hwu +2 more
exaly +2 more sources
OTG-snpcaller: An Optimized Pipeline Based on TMAP and GATK for SNP Calling from Ion Torrent Data [PDF]
PLoS ONE, 2014 Because the new Proton platform from Life Technologies produced markedly different data from those of the Illumina platform, the conventional Illumina data analysis pipeline could not be used directly.
Xun Xu
exaly +2 more sources
Whole genome sequence data on Ethiopian key sorghum landraces and founder lines [PDF]
Data in BriefSorghum ( Sorghum bicolor (L.) Moench) is the fifth most important cereal globally. Its genetic diversity is key to improving yield stability, stress tolerance, and adaptation to different environments.
Meseret Wondifraw +9 more
doaj +2 more sources
Pangenomes aid accurate detection of large insertions and deletions from targeted sequencing: the case of cardiomyopathies [PDF]
Genome MedicineBackground Gene panels represent a widely used strategy for genetic testing in a vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection of short coding variants, it often fails to detect many larger variants.
Francesco Mazzarotto +31 more
doaj +2 more sources
GermVarX: A Robust Workflow for Joint Germline Variant Exploration in whole-exome sequencing cohorts. [PDF]
PLoS ONEAccurate identification of germline variants from whole-exome sequencing (WES) data is foundational to population genetics, disease association studies, and clinical genomics.
Thao Thi Phuong Nguyen +7 more
doaj +2 more sources
Accelerating next generation sequencing data analysis: an evaluation of optimized best practices for Genome Analysis Toolkit algorithms [PDF]
Genomics & Informatics, 2020 Advancements in next generation sequencing (NGS) technologies have significantly increased the translational use of genomics data in the medical field as well as the demand for computational infrastructure capable processing that data.
Karl R. Franke, Erin L. Crowgey
doaj +1 more source
Detailed comparison of two popular variant calling packages for exome and targeted exon studies [PDF]
PeerJ, 2014 The Genome Analysis Toolkit (GATK) is commonly used for variant calling of single nucleotide polymorphisms (SNPs) and small insertions and deletions (indels) from short-read sequencing data aligned against a reference genome.
Charles D. Warden +3 more
doaj +2 more sources
Scientific Reports, 2022 Rapid advances in high-throughput DNA sequencing technologies have enabled the conduct of whole genome sequencing (WGS) studies, and several bioinformatics pipelines have become available.
Raphael O. Betschart +8 more
doaj +1 more source
Variant callers for next-generation sequencing data: a comparison study. [PDF]
PLoS ONE, 2013 Next generation sequencing (NGS) has been leading the genetic study of human disease into an era of unprecedented productivity. Many bioinformatics pipelines have been developed to call variants from NGS data.
Xiangtao Liu +4 more
doaj +1 more source